Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)

Abstract

MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in the
regulation of gene expression in eukaryotes. Gene expression involves post-transcriptional
gene regulation by miRNAs. miRNAs are formed from precursor RNA molecules that fold into
a stem loop secondary structure. The mature miRNA is one end of the precursor miRNA,
defined by the cut from ‘Drosha’ on either the 5’ or 3’ arm. In this study, we have used a
bioinformatics approach to identify miRNAs in 3,361 contigs obtained from partial genome
sequence data of Abelmoschus esculentus (okra) sequenced by NGS technology. Using C-mii
and psRNA Target tools, we identified two miRNAs and their target RNAs for which a regulatory
miRNA binding has been verified. Their targets consisted of transcription factors involved in
growth and development, gene regulation and metabolism. Phylogenetic analysis of the newly
identified miRNA family has been done to compare their level of conservation with respect to
the other members of the plant kingdom.